Errors when identifers dont match shape, + whitespace

fluents/dataset.py

@@ -36,28 +36,30 @@ class Dataset:
 
     data = Dataset(rand(10,20)) (generates dims and ids (no links))
     """
-    def __init__(self,array,identifiers=None,name='Unnamed dataset'):
+    def __init__(self, array, identifiers=None, name='Unnamed dataset'):
         self._dims = [] #existing dimensions in this dataset
         self._map = {} # internal mapping for dataset:  identifier <--> index
         self._name = name
         self._identifiers = identifiers
         self._type = 'n'
-        try:
-            array = atleast_2d(asarray(array))
-        except:
-            print "Cant cast array as numpy-array"
-            return
-        # vectors are column vectors 
-        if array.shape[0]==1:
-            array = array.T
-        self.shape = array.shape
 
+        if len(array.shape)==1:
+            array = atleast_2d(asarray(array))
+            # vectors are column vectors 
+            if array.shape[0]==1:
+                array = array.T
+        self.shape = array.shape
         if identifiers!=None:
-            self._set_identifiers(identifiers,self._all_dims)
+            identifier_shape = [len(i[1]) for i in identifiers]
+            if len(identifier_shape)!=len(self.shape):
+                raise ValueError, "Identifier list length must equal array dims"
+            for ni, na in zip(identifier_shape, self.shape):
+                if ni!=na:
+                    raise ValueError, "identifier-array mismatch in %s: (idents: %s, array: %s)" %(self._name, ni, na)
+            self._set_identifiers(identifiers, self._all_dims)
         else:
-            self._identifiers = self._create_identifiers(self.shape,self._all_dims)
+            self._identifiers = self._create_identifiers(self.shape, self._all_dims)
-            self._set_identifiers(self._identifiers,self._all_dims)
+            self._set_identifiers(self._identifiers, self._all_dims)
-            
         self._array = array
 
     def __iter__(self):
@@ -94,17 +96,16 @@ class Dataset:
             all_dims.add(dim_suggestion)
         return ids
 
-    def _set_identifiers(self,identifiers,all_dims):
+    def _set_identifiers(self, identifiers, all_dims):
         """Creates internal mapping of identifiers structure."""
-        for dim,ids in identifiers:
+        for dim, ids in identifiers:
             pos_map = ReverseDict()
             if dim not in self._dims:
                 self._dims.append(dim)
                 all_dims.add(dim)
             else:
                 raise ValueError, "Dimension names must be unique whitin dataset"
-            
+            for pos, id in enumerate(ids):
-            for pos,id in enumerate(ids):
                 pos_map[id] = pos
             self._map[dim] = pos_map
             
@@ -121,11 +122,10 @@ class Dataset:
         """Returns the numeric array (data) of dataset"""
         return self._array
 
-    def add_array(self,array):
+    def add_array(self, array):
         """Adds array as an ArrayType object.
         A one-dim array is transformed to a two-dim array (row-vector)
         """
-        
         if self.shape!=array.shape:
             raise ValueError, "Input array must be of similar dimensions as dataset"
         self._array = atleast_2d(asarray(array))
@@ -138,7 +138,7 @@ class Dataset:
         """Returns all dimensions in project"""
         return self._all_dims
 
-    def get_dim_name(self,axis=None):
+    def get_dim_name(self, axis=None):
         """Returns dim name for an axis, if no axis is provided it
         returns a list of dims"""
         if type(axis)==int:
@@ -178,7 +178,6 @@ class Dataset:
         You can optionally provide a list of identifiers to retrieve a
         index subset.
         
-        
         Identifiers are the unique names (strings) for a variable in a
         given dim.  Index (Indices) are the Identifiers position in a
         matrix in a given dim.  If none of the input identifiers are
@@ -218,8 +217,8 @@ class CategoryDataset(Dataset):
     .
     """
     
-    def __init__(self,array,identifiers=None,name='C'):
+    def __init__(self, array, identifiers=None, name='C'):
-        Dataset.__init__(self,array,identifiers=identifiers,name=name)
+        Dataset.__init__(self, array, identifiers=identifiers, name=name)
         self.has_dictlists = False
         self._type = 'c'
             
@@ -229,7 +228,7 @@ class CategoryDataset(Dataset):
         ex: data['gene_id'] = ['map0030','map0010', ...]
         """
         data={}
-        for name,ind in self._map[self.get_dim_name(0)].items():
+        for name, ind in self._map[self.get_dim_name(0)].items():
             data[name] = self.get_identifiers(self.get_dim_name(1),
                                               list(self._array[ind,:].nonzero()))
         self._dictlists = data
@@ -240,7 +239,7 @@ class CategoryDataset(Dataset):
         """Returns data as a list of Selection objects.
         """
         ret_list = []
-        for cat_name,ind in self._map[self.get_dim_name(1)].items():
+        for cat_name, ind in self._map[self.get_dim_name(1)].items():
             ids = self.get_identifiers(self.get_dim_name(0),
                                        self._array[:,ind].nonzero()[0])
             selection = Selection(cat_name)
@@ -254,26 +253,26 @@ class GraphDataset(Dataset):
 
     A dataset class for representing graphs using an (weighted)
     adjacency matrix
-    (aka. restricted to square symmetric matrices)
+    (restricted to square symmetric matrices)
     
     If the library NetworkX is installed, there is support for
     representing the graph as a NetworkX.Graph, or NetworkX.XGraph structure.
     """
     
-    def __init__(self,array=None,identifiers=None,shape=None,all_dims=[],**kwds):
+    def __init__(self, array=None, identifiers=None, shape=None, all_dims=[],**kwds):
-        Dataset.__init__(self,array=array,identifiers=identifiers,name='A')
+        Dataset.__init__(self, array=array, identifiers=identifiers, name='A')
         self._graph = None
         self._type = 'g'
         
-    def asnetworkx(self,nx_type='graph'):
+    def asnetworkx(self, nx_type='graph'):
         dim = self.get_dim_name()[0]
-        ids = self.get_identifiers(dim,sorted=True)
+        ids = self.get_identifiers(dim, sorted=True)
         adj_mat = self.asarray()
-        G = self._graph_from_adj_matrix(adj_mat,labels=ids)
+        G = self._graph_from_adj_matrix(adj_mat, labels=ids)
         self._graph = G
         return G
     
-    def _graph_from_adj_matrix(self,A,labels=None):
+    def _graph_from_adj_matrix(self, A, labels=None):
         """Creates a networkx graph class from adjacency
         (possibly weighted) matrix and ordered labels.
         
@@ -286,7 +285,7 @@ class GraphDataset(Dataset):
         except:
             print "Failed in import of NetworkX"
             return
-        m,n = A.shape# adjacency matrix must be of type that evals to true/false for neigbours
+        m, n = A.shape# adjacency matrix must be of type that evals to true/false for neigbours
         if m!=n:
             raise IOError, "Adjacency matrix must be square"
 
@@ -298,17 +297,18 @@ class GraphDataset(Dataset):
         if labels==None: # if labels not provided mark vertices with numbers
             labels = [str(i) for i in range(m)]
 
-        for nbrs,head in izip(A,labels):
+        for nbrs, head in izip(A, labels):
-            for i,nbr in enumerate(nbrs):
+            for i, nbr in enumerate(nbrs):
                 if nbr:
                     tail = labels[i]
                     if type(G)==nx.XGraph:
-                        G.add_edge(head,tail,nbr)
+                        G.add_edge(head, tail, nbr)
                     else:
-                        G.add_edge(head,tail)
+                        G.add_edge(head, tail)
         return G
         
-Dataset._all_dims=set()
+Dataset._all_dims = set()
+
 
 class ReverseDict(dict):
     """
@@ -336,30 +336,34 @@ def to_file(filepath,dataset,name=None):
     """
     if not name:
         name = dataset._name
-    data = shelve.open(filepath,flag='c',protocol=2)
+    data = shelve.open(filepath, flag='c', protocol=2)
     if data: #we have an append 
         names = data.keys()
         if name in names:
             print "Data with name: %s overwritten" %dataset._name
-    sub_data = {'array':dataset._array,'idents':dataset._identifiers,'type':dataset._type}
+    
+    sub_data = {'array':dataset._array,
+                'idents':dataset._identifiers,
+                'type':dataset._type}
     data[name] = sub_data 
     data.close()
 
 def from_file(filepath):
-    """Read dataset from file """
+    """Read dataset(s) from file """
-    data = shelve.open(filepath,flag='r')
+    data = shelve.open(filepath, flag='r')
     out_data = []
     for name in data.keys():
         sub_data = data[name]
         if sub_data['type']=='c':
-            out_data.append(CategoryDataset(sub_data['array'],identifiers=sub_data['idents'],name=name))
+            out_data.append(CategoryDataset(sub_data['array'], identifiers=sub_data['idents'], name=name))
         elif sub_data['type']=='g':
-            out_data.append(GraphDataset(sub_data['array'],identifiers=sub_data['idents'],name=name))
+            out_data.append(GraphDataset(sub_data['array'], identifiers=sub_data['idents'], name=name))
         else:
-            out_data.append(Dataset(sub_data['array'],identifiers=sub_data['idents'],name=name)) 
+            out_data.append(Dataset(sub_data['array'], identifiers=sub_data['idents'], name=name)) 
             
     return out_data
-    
+
+
 class Selection(dict):
     """Handles selected identifiers along each dimension of a dataset"""